Biodecolorization by microorganisms is a potential treatment technique because they seem to be environmentally safe. In the present study, the decolorization and detoxification of cotton blue, crystal violet, malachite green and methyl violet by endophytic fungi were investigated. Preliminary screening result indicated that SWUSI4, identified as Bjerkandera adusta, demonstrated the best decolorization for the four TPM dyes within 14 days. Furthermore, optimization result demonstrated the decolorization rate could reach above 90% at 24 h by live cells of isolate SWUSI4 when 4 g biomass was added into 100-mL dyes solution with the concentration 50 mg/L and shaking (150 rpm) conditions. Moreover, decolorization mechanism analysis shows that the decolorization was caused by the isolate SWUSI4 that mainly includes both absorption of biomass and/or degradation of enzymes. Biosorption of dyes was attributed to binding to hydroxyl, amino, phosphoryl alkane, and ester–lipids groups based on Fourier transform infrared (FTIR) analyses. The biodegradation potential of SWUSI4 was further suggested by the change of peaks in the ultraviolet–visible (UV–vis) spectra and detection of manganese peroxidase and lignin peroxidase activities. Finally, the phytotoxicity test confirmed that the toxicity of TPM dyes after treatment with SWUSI4 was significantly lower than that before treatment. These results indicate that an endophytic SWUSI4 could be used as a potential TPM dyes adsorption and degradation agent, thus facilitating the study of the plant–endophyte symbiosis in the bioremediation processes.